BN1730 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 8.2101e-08 9.5399e-05
Layer 4 1.1618e-06 3.5140e-05
Layer 2 1.7451e-06 3.4375e-03
Layer 5 1.6629e-05 3.3532e-04
Layer 6 3.8691e-05 3.5849e-03
Layer 1 1.6356e-01 3.1296e-01
WM 9.9998e-01 7.8836e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
CHGA Expression Distribution
Gene Specificity Score (GSS)
CHGA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
CHGA Layer 4 2.8145 0.8202
ATP6V1B2 Layer 4 2.7363 0.8049
ATP2B2 Layer 4 2.9473 0.8016
KLHDC3 Layer 5 2.7070 0.8014
SCG5 Layer 5 2.5176 0.8006
RTL8C Layer 3 2.4668 0.7993
PGK1 Layer 4 2.5449 0.7992
SEZ6L2 Layer 5 2.7715 0.7985
AMPH Layer 4 2.5273 0.7983
TMEM130 Layer 4 2.7246 0.7977
TUBB Layer 5 2.6660 0.7974
CABP1 Layer 4 2.6191 0.7972
FKBP8 Layer 4 2.6484 0.7970
SH3GL2 Layer 4 2.6543 0.7967
SV2A Layer 3 2.5176 0.7963
MEF2C Layer 4 2.7539 0.7963
ATP6V1G2 Layer 5 2.5508 0.7956
RAB3A Layer 3 2.5332 0.7952
GNG3 Layer 5 2.5605 0.7944
GUCY1B1 Layer 4 2.4727 0.7934
NAPA Layer 4 2.5059 0.7933
KIF3C Layer 5 2.5215 0.7932
TERF2IP Layer 4 2.6367 0.7928
GABRA1 Layer 3 2.6074 0.7928
YPEL3 Layer 4 2.6602 0.7924
PINK1 Layer 4 2.6719 0.7917
PNMA8A Layer 4 2.8828 0.7915
ATP1A3 Layer 4 2.7188 0.7912
FAIM2 Layer 4 2.5957 0.7906
SNCA Layer 5 2.6602 0.7900
TOMM20 Layer 4 2.6484 0.7897
PRDX2 Layer 4 2.5605 0.7896
STX1B Layer 4 2.8711 0.7891
GABARAPL1 Layer 5 2.6777 0.7891
INA Layer 4 2.7070 0.7891
KIF1A Layer 4 2.6309 0.7890
PARK7 Layer 4 2.5391 0.7890
RHBDD2 Layer 5 2.5957 0.7889
MAGED1 Layer 4 2.5273 0.7889
CAPNS1 Layer 4 2.5117 0.7882
PPP2R1A Layer 4 2.6074 0.7881
INPP5F Layer 4 3.0254 0.7880
VDAC1 Layer 4 2.5781 0.7879
PCMT1 Layer 3 2.5215 0.7876
GHITM Layer 5 2.6484 0.7874
USP22 Layer 4 2.5508 0.7872
SNCB Layer 4 2.7539 0.7871
BMERB1 Layer 4 2.8027 0.7870
NDUFB9 Layer 5 2.6426 0.7869
RABAC1 Layer 5 2.5059 0.7864

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1730
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1730_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1730/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1730/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1730/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1730/report/PD/BN1730_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1730/report/PD/BN1730_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 06:12:20
  • Number of Processes: 10
  • Spending Time: 0h 4m